Season 2 because most of my favorite episodes are in there (Lesson Zero, Read it And Weep, and a few others) -- plus, it had some of
the prettiest screenshots ever. And the songs were fantastic. And Discord and Queen Chrysalis! Yes!
Season 1 was a close second, though.
Season 3 is not second because I:
-- Didn't really want to see a 'reformed' Discord
-- Not very many episodes
-- Twilicorn -- because now all of my Twi - ships seem ridiculous except for TwiMac.